Use SST's (special service tools) for the axle input section if you are going to be moving the tranny around. I used two pieces of wooden dowel rod to hold the spider gear in place as shown in the picture.
Nice and clean so it won't slip out of your hands, and, it's always nice to clean things before you put them back in.
Now is a good time to refurbish your axles.
http://www.mx6.com/forums/showthread.php?t=98744 (1st gen PROJECT: Rebuilding Your Axles)
Remove the rear main seal, pilot bearing, metal plate behind the flywheel and clean well with brake cleaner. You won't be replacing the gasket behind the rear main seal bracket unless you also plan on removing and re-sealing the oil pan as well, notice that there are two 10mm bolts from the oil pan into the bracket itself.
I wonder why the seal was leaking?
Ahhh, a brand new seal.
Rear main seal and pilot bearing installed.
When you install the rear main seal, you should use some permatex super sealant. It isnt an RTV thick type sealant, rather a thin water like sealant for making paper thin gaskets. It comes in a can with a brush and looks similar to a rubber cement container. You want to put a SMALL amount around the outside diameter of the seal and a a small around of grease on the inside diameter of the seal.
Pressure plate and disk installed and ready for transaxle.
Throwout bearing installed.
Installation is the opposite of removal, you don't HAVE to do it the way I did it. There are plenty of options as far as WHAT to take off, I chose to take everything that I could, but that doesnt mean that you have to as well.
Ahhhh, now it's looking better and almost ready to be fired up.
Make sure that you break the clutch in before going crazy on it, otherwise you'll be doing it again.
